Ok, good info. We seem to have the exact same hardware combination: iMac, Mac OS X Lion and the first version of the MOTU UltraLite.
I'm not using Logic at all. I'm experiencing the issue in all applications, Ableton Live, iTunes, VLC player, QuickTime Player, the browser etc.
Have you experienced the issue in other applications than Logic? If not, can you do a test, for instance play music through iTunes for an hour or two and see if the issue shows up? What is your frequency of the issue?
I'm almost sure this is a software issue - either a MOTU driver issue og a Mac OS X Lion issue. I have done a lot of troubleshooting including:
1. Tried several firewire cables (To exlude that it's not a bad cable) - no luck
2. Connecting only one firewire unit - the UltraLite (To exclude that other firewire units are causing the issue) - no luck
3. Tried the UltraLite on my Mac OS Tiger machine - no issue, I cannot reproduce the issue on this machine
4. Tried to only run one application after a fresh restart: iTunes (to exclude that some third party application is causing the issue) - no luck
5. It worked fine on my iMac running Snow Leopard before upgrading to Lion
6. We are two persons with the same hardware combination experiencing the exact same issue (Kinda proves that its not a broken sound interface)
7. Downgraded to an earlier MOTU driver than the newest so-called "Lion compatible" driver - no luck
8. The issue is only when the UltraLite is connected. There is no issue when running the native sound output or another USB sound interface (I have tried a Guitar rig session I/O on my iMac)
9. The issue stops if I restart the sound interface or restarts Lion or switch the sample rate in the MOTU Audio Setup
Unfortunately I have not another Lion Machine to test on (to exclude that it's some hidden applications running in the background causing the issue). Do you have other Lion machines to test on?
If you have the time you can try to do the same troubleshooting as me. If you conclude the same as me I think we have a good bug report to Apple/MOTU that they hopefully will take care of.
BR, Rasmus